|
2 | 2 |
|
3 | 3 | A toolkit for semantic segmentation of volumetric data using PyTorch deep learning models.
|
4 | 4 |
|
5 |
| - |
| 5 | +  |
6 | 6 |
|
7 |
| -Given a 3d image volume and corresponding dense labels (the segmentation), a 2d model is trained on image slices taken along the x, y, and z axes. The method is optimised for small training datasets, e.g a single $384^3$ pixel dataset. To achieve this, all models use pretrained encoders and image augmentations are used to expand the size of the training dataset. |
| 7 | +Given a 3d image volume and corresponding dense labels (the segmentation), a 2d model is trained on image slices taken along the x, y, and z axes. The method is optimised for small training datasets, e.g a single dataset in between $128^3$ and $512^3 $pixels. To achieve this, all models use pre-trained encoders and image augmentations are used to expand the size of the training dataset. |
8 | 8 |
|
9 |
| -This work utilises the abilities afforded by the excellent [segmentation-models-pytorch](https://github.com/qubvel/segmentation_models.pytorch) library. Also the metrics and loss functions used make use of the hard work done by Adrian Wolny in his [pytorch-3dunet](https://github.com/wolny/pytorch-3dunet) repository. |
| 9 | +This work utilises the abilities afforded by the excellent [segmentation-models-pytorch](https://github.com/qubvel/segmentation_models.pytorch) library in combinations with augmentations made available via [Albumentations](https://albumentations.ai/). Also the metrics and loss functions used make use of the work done by Adrian Wolny in his [pytorch-3dunet](https://github.com/wolny/pytorch-3dunet) repository. |
10 | 10 |
|
11 | 11 | ## Requirements
|
12 | 12 |
|
@@ -44,4 +44,15 @@ The input data will be segmented using the input model following the settings sp
|
44 | 44 |
|
45 | 45 | ## Using the API
|
46 | 46 |
|
47 |
| -You can use the functionality of the package in your own program via the API, this is [documented here](https://diamondlightsource.github.io/volume-segmantics/). This interface is the one used by [SuRVoS2](https://github.com/DiamondLightSource/SuRVoS2), a client/server GUI application that allows fast annotation and segmentation of volumetric data. |
| 47 | +You can use the functionality of the package in your own program via the API, this is [documented here](https://diamondlightsource.github.io/volume-segmantics/). This interface is the one used by [SuRVoS2](https://github.com/DiamondLightSource/SuRVoS2), a client/server GUI application that allows fast annotation and segmentation of volumetric data. |
| 48 | + |
| 49 | +## References |
| 50 | + |
| 51 | +**Albumentations** |
| 52 | +Buslaev, A., Iglovikov, V.I., Khvedchenya, E., Parinov, A., Druzhinin, M., and Kalinin, A.A. (2020). Albumentations: Fast and Flexible Image Augmentations. Information 11. [https://doi.org/10.3390/info11020125](https://doi.org/10.3390/info11020125) |
| 53 | + |
| 54 | +**Segmentation Models PyTorch** |
| 55 | +Yakubovskiy, P. (2020). Segmentation Models Pytorch (GitHub). |
| 56 | + |
| 57 | +**PyTorch-3dUnet** |
| 58 | +Wolny, A., Cerrone, L., Vijayan, A., Tofanelli, R., Barro, A.V., Louveaux, M., Wenzl, C., Strauss, S., Wilson-Sánchez, D., Lymbouridou, R., et al. (2020). Accurate and versatile 3D segmentation of plant tissues at cellular resolution. ELife 9, e57613. [https://doi.org/10.7554/eLife.57613](https://doi.org/10.7554/eLife.57613). |
0 commit comments